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Magnesium in PDB 2yy2: Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx

Enzymatic activity of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx

All present enzymatic activity of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx:
3.1.4.35;

Protein crystallography data

The structure of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx, PDB code: 2yy2 was solved by N.Handa, M.Shirouzu, T.Terada, K.Omori, J.Kotera, S.Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 2.80
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.270, 104.270, 269.610, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24

Other elements in 2yy2:

The structure of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx (pdb code 2yy2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx, PDB code: 2yy2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2yy2

Go back to Magnesium Binding Sites List in 2yy2
Magnesium binding site 1 out of 2 in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1102

b:30.6
occ:1.00
OD1 A:ASP293 2.6 30.8 1.0
O A:HOH1112 3.1 24.7 1.0
OE2 A:GLU322 3.4 30.5 1.0
CG A:ASP293 3.7 28.3 1.0
OG1 A:THR363 3.8 19.8 1.0
NE2 A:HIS325 3.8 28.9 1.0
ZN A:ZN101 3.9 55.6 1.0
CD2 A:HIS325 4.1 28.2 1.0
OD2 A:ASP293 4.2 29.0 1.0
O A:HIS292 4.3 28.6 1.0
O A:THR363 4.3 29.0 1.0
CD A:GLU322 4.4 28.4 1.0
OD2 A:ASP402 4.5 28.0 1.0
CD2 A:HIS292 4.5 27.9 1.0
CB A:THR363 4.5 22.7 1.0
CG A:GLU322 4.5 26.9 1.0
CD2 A:HIS296 4.7 32.0 1.0
NE2 A:HIS292 4.8 28.1 1.0
C A:THR363 4.9 27.5 1.0
CD2 A:HIS252 5.0 29.9 1.0
CB A:ASP293 5.0 25.3 1.0
CE1 A:HIS325 5.0 29.3 1.0

Magnesium binding site 2 out of 2 in 2yy2

Go back to Magnesium Binding Sites List in 2yy2
Magnesium binding site 2 out of 2 in the Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain Complexed with Ibmx within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1104

b:26.3
occ:1.00
OD1 B:ASP293 2.6 35.7 1.0
OE2 B:GLU322 3.5 24.8 1.0
OG1 B:THR363 3.6 28.7 1.0
CG B:ASP293 3.6 33.7 1.0
ZN B:ZN103 3.7 59.9 1.0
OD2 B:ASP293 3.9 36.4 1.0
NE2 B:HIS325 4.0 32.5 1.0
CD2 B:HIS325 4.2 31.8 1.0
O B:THR363 4.2 32.6 1.0
CD2 B:HIS292 4.3 32.3 1.0
O B:HOH1124 4.3 23.0 1.0
O B:HIS292 4.3 36.4 1.0
CB B:THR363 4.4 27.8 1.0
CD B:GLU322 4.5 23.3 1.0
CD2 B:HIS296 4.6 30.0 1.0
OD2 B:ASP402 4.7 39.3 1.0
CD2 B:HIS252 4.7 36.2 1.0
CG B:GLU322 4.8 21.6 1.0
NE2 B:HIS292 4.8 32.1 1.0
NE2 B:HIS252 4.8 38.0 1.0
C B:THR363 4.9 30.6 1.0
CB B:ASP293 5.0 31.5 1.0

Reference:

N.Handa, M.Shirouzu, T.Terada, K.Omori, J.Kotera, S.Yokoyama. Crystal Structure of the Human Phosphodiesterase 9A Catalytic Domain To Be Published.
Page generated: Mon Dec 14 07:49:41 2020

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